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generally ad runes give u better early game while armor pen give u a better mid to end game but since most adc build last whisper anyways ad runes are generally better.
armor pen's better for champions if not planning on buying a percentage pen item.

Let's make up a random champion that has random abilities and scaling, with a generic AD offensive mastery set at level 2 where they have 2 abilities. I'm not going to bother with looking these up for an actual champ, but you can re-do the math with different assumptions:

Autoattack (AA): 55+AD damage
Q: 65+AD damage
W: 60+0.75*AD damage

This champ has an average AD scaling on abilities.

Masteries:

+5 AD
6 flat ArPen

The enemy champ isn't stupid and brings armor runes with the 6 points from masteries to top lane, so somewhere around 30-35 armor IIRC. Let's say 35.

So, in a generic level 2 analysis of pew pew hurr hurr pew pew, They are pretty damn close to even, although ArPen edges out slightly.

Other mathematical characteristics of ArPen based on the formula:

- The closer [EnemyArmor - ArPen] is to 0, the more value the ArPen actually is. See a previous poster who mentioned effective HP -- chopping off 100 EHP when the target has 2000 EHP is much less valuable than chopping 100 off when they have 1000 EHP. So lower armor = arpen is stronger.

- ArPen will not drop armor before 0. It's Pen, not Shred. Every point of ArPen that exceeds the target's actual Armor is completely wasted. This generally doesn't matter for champs except in very weird situations. However, this means that ArPen is almost always wasted for creep killing, unless you are AD jungling at level 1.

- Champs gain armor every level, and will generally actually buy armor throughout the game (or get it via Aegis buff or w/e). Hence, champs generally become stronger against small doses of ArPen (LIKE ArPen MARKS) in mid and late game.

General recommendations (all assume you are an AD champ with physical damage abilities that have some AD scaling):

1. If you are not ultra pro last-hitting savant, AD runes will help.
2. If you want to make the biggest champ-killing plays at level 1-3, ArPen is a decent consideration.
3. If you plan on never getting Last Whisper, and you want to really stack your early game with more early game power (you lean towards Brutalizer as an item pick), then ArPen is a decent consideration.
4. If Last Whisper is a legit item for your build, don't bother with flat ArPen runes and get AD instead.
5. If maximal creep farm is important to you in laning, lean towards AD.

There are other specific detailed cases, but they are specific and detailed. To be honest, I consider AD runes the go-to in the vast majority of cases, if only for the more reliable last-hits. The champ damage is close to a wash in general. If you stack ArPen quints on top, you can achieve maybe 3% more damage than the AD set in the first 1-3 levels. If you continue with ArP stacking, you may achieve up to 10% more damage by midgame, perhaps (e.g. your personal ArP + Brutalizer to almost perfectly meet enemy champ Armor levels).

Edit:

Oh yeah, rule #6:

If your champ has non-damage abilities that scale off AD (RIVEN SHIELD LULZ), then uh, Arpen has much less value ~_~.

Comparison
Now why did I mention the difference between the two? Because if you take Flat Penetration along side Percent Penetration, the total amount or armor you ignore is reduced by Flat pen. first, then percent. So you will waste your own resources against armor because if an enemy has 66 armor, you build 15 Arpen from runes (Runes only have flat pen available), 10% arpen (From Weapon Expertise), and the Black Cleaver, you will only take out 62(ish) damage, instead of 66 you could've shreded if you had put 3 points into Sunder, Sure thats not a fair matchup, but at least you see the difference between flat and percent Arpen.

So with that in mind, don't actually take Flat Arpen runes with champions like J4, who have innate percent armor shred in their ability kits. Some other champions that have percent armor shred are Urgot, Wukong, Shyvana, among others.

I know this post is rather old, but this is wrong AS of current for anyone else reading this.
In fact, flat Arpen (from runes and masteries and such) is actually BETTER on champs who have armor % shreds. The reason is, it basicly works how it used to this way, and the way riot is changing it back to. Reducing a % first, then flat is basicly amplifying your flat pen.

TLDR; If the champ has innate armor shred %, Arpen runes are usually the way to go.